diff options
| -rw-r--r-- | doc/pattern_sim.txt | 20 | ||||
| -rw-r--r-- | doc/symmetry.txt | 15 |
2 files changed, 20 insertions, 15 deletions
diff --git a/doc/pattern_sim.txt b/doc/pattern_sim.txt index e69de29b..f70123e1 100644 --- a/doc/pattern_sim.txt +++ b/doc/pattern_sim.txt @@ -0,0 +1,20 @@ +pattern_sim does not know about symmetry, so your input reflection list +(give with "-i") must be expanded. You can do this with: + +$ get_hkl -i myfile.hkl -o output.hkl -y mypointgroup -e 1 + + + +The symmetry of the molecular model (the space group) +----------------------------------------------------- + +get_hkl does not currently understand symmetry, which means you'll have to +expand any molecular model (the PDB) out to P1 to get the correct results. You +can achieve that, for example, by loading it into Mercury, turning on "Packing" +and re-saving. Alternatively, you can do this using CCP4 with a command like: + +$ echo symgen P63 | pdbset xyzin model.pdb xyzout model-P1.pdb + +While on this subject, you might also want to include hydrogens in the model +using something like: +$ echo HYDROGENS APPEND | hgen xyzin model.pdb xyzout model-with-H.pdb diff --git a/doc/symmetry.txt b/doc/symmetry.txt index 4deafa35..451c4922 100644 --- a/doc/symmetry.txt +++ b/doc/symmetry.txt @@ -47,18 +47,3 @@ returns (by reference) the indices of the "n"th equivalent reflection. You just have to worry about the general position, because get_equiv() will work out the special positions for you. get_general_equiv() must return the original indices when idx=0. - - -The symmetry of the molecular model (the space group) ------------------------------------------------------ - -get_hkl does not currently understand symmetry, which means you'll have to -expand any molecular model (the PDB) out to P1 to get the correct results. You -can achieve that, for example, by loading it into Mercury, turning on "Packing" -and re-saving. Alternatively, you can do this using CCP4 with a command like: - -$ echo symgen P63 | pdbset xyzin model.pdb xyzout model-P1.pdb - -While on this subject, you might also want to include hydrogens in the model -using something like: -$ echo HYDROGENS APPEND | hgen xyzin model.pdb xyzout model-with-H.pdb |